For me, it's the scene at the beginning where Zak wakes up and we first take control of him. I've never seen that in a game before or sinse; having the opportunity to explore the main character's home. We learn a lot about him in those early scenes.

It reminds me of The Hitchhiker's Guide to the Galaxy, which begins with Arthur Dent waking up in his room hung over; completely oblivious to the fact that his home and planet are about to be destroyed.